The Nature Trail

Modern chemistry and biochemistry are hard to understand without 3D models. In this article, we look at programs that bring order to the chaos of connected atoms by arranging them in functional sections and in three dimensions.

Finding a science that has made such rapid progress in recent decades as biochemistry is difficult. Computer technology is an indispensable tool: Many biochemical processes cannot be understood until you create a three-dimensional molecular image of the active substances to illustrate their reactions.

The keyword "molecule" returns 10 entries in the Ubuntu Software Center, including one game and two drawing programs for chemical structures. But, you also will find a number of useful modeling programs, including the classic RasMol tool, the all-rounder PyMOL, the master builder Avogadro, the Jmol Java program (which runs anywhere, even in your browser), and an outsider named GChemPaint.

The most promising program, Ghemical, which not only can represent molecules but also can compute molecular orbitals, failed to make it into the test: After the install, it crashed with a number of error messages. In fact, all of the relevant forums also report installation problems with Ghemical on Ubuntu.

What the Programs Offer

Chemical formulas are something like the technical language of chemistry. Originally, scientists used the molecular formula, a simple string of letters and numbers for the elements and their numbers in the molecule. Later on, the two-dimensional structural formula yielded significantly more information about the molecule, such as the existence of single and double bonds.

Visualization programs now add scale to the structural formula (Figure 1). The atoms appear in their correct positions and can be viewed from different directions. Additionally, depending on the program that is used, you can also display molecular surfaces, functional components, or electron density maps. What looks a little like technical overkill in the simple ethylene molecule in Figure 1 turns out to be extremely helpful with complex molecules such as DNA.

Figure 1: The various representations of the simple hydrocarbon molecule, ethylene, from the simple molecular formula through a structural formula, to visualization.

Representing the electron distribution around the nuclear framework of the molecule is another excellent capability of molecular visualization: If you want to understand how electrostatic attraction and repulsion processes act within the molecule, an electron density map is a big help. To generate it, you can call on the Electron Density Server at Uppsala University [1]. The process is complicated, but it works – as Figure 2 shows – if you follow the instructions [2]; I generated this image with PyMOL.

Figure 2: Electron density, as calculated by the Electron Density Server at Uppsala University, is the space around the atomic structure of the molecule in which an electron can reside.

The following brief summary highlights some applications, but they will not reveal their impressive visualization capabilities until you perform your own experiments. If you are interested, you should check out the power of moving molecular images yourself. Specifically, the DNS representation on the Biomodel site by Angel Herráez at Universidad de Alcalá, Spain [3], is a good starting point for understanding the potential, especially for biology lessons in secondary schools.

RasMol, the Classic Tool

RasMol [4] was the first molecular visualization program for Linux (Figure 3). The Gtk-based version discussed here (version 2.7.5) impresses by not being overly complex and allowing quick switching from one view to the next. Rotate and zoom processes are intuitive after a short time, and RasMol tutorials are available online [5].

Figure 3: The "Klenow enzyme," a protein fragment of DNA polymerase I of the Escherichia coli bacteria, in the RasMol ribbon view with fragment coloration. Newer visualization programs resolve the blue strip into molecular chains.

Simultaneous loading of multiple molecules is possible. After selecting the visible molecule, you can change its appearance and position, thus illustrating the interaction of several molecules in synthetic processes, for example.

RasMol runs not only on Linux, but also on Mac OS X and Windows – but only on the desktop. This means you cannot create web tutorials, which are so meaningful in education.

Jmol, the Multipurpose Tool

Jmol, written in Java [6], can be used both on the desktop and integrated with HTML pages as an applet. Thus, it allows for interactive tutorials that let you put together ideal interactive learning units for upper-level classes.

Many great examples relating to DNA are available online from the Spanish Biomodel website I mentioned before [7]. Thanks to Java, Jmol runs as a desktop application on almost any operating system, offering a clear-cut, intuitive user interface (Figure 4).

Figure 4: Once again, the Klenow fragment, this time illustrated in Jmol with fragment coloration. Unlike RasMol, Jmol resolves the blue strip into molecular chains.

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